The paper assessed agricultural production systems from a sustainability perspective defined in terms of relatively homogeneous agro-ecological zones of Africa, using the framework of a production function. Data used were drawn from FAOSTAT, the National Centre for Atmospheric Research and World Bank Indicators respectively for the period 1961-2009. The data were separated into three sub periods, namely: entire period (1961-2009), the pre-Structural Adjustment Period (SAP) reform period (1961-1985) and the post SAP reform period (1986-2009). This was necessitated by the need to examine whether production systems may have been shifted out of the overall trajectory of system evolution by shocks e.g. policy (SAP) among others. To investigate whether there has been a degradation of the quality of the natural resource base across the diverse agro-ecological zones; the estimated TFP trends were related to changes in selected resource quality variables over time. The results showed that the Northern and Southern agro-ecological zones had non-negative trends in TFP, indicating sustainability of production systems. However, the result indicated that the policy instrument (structural adjustment programme) may have shifted farming or production systems out of the overall trajectory of system evolution in three out of the five agro-ecological zones studied which showed negative TFP trends. A degradation of resource quality over time was noted during the pre-SAP reform period, but was maintained during the post-SAP period.